Amazon doesn't want companies to use this to prevent third parties from selling their products obtained via other channels through Amazon by claiming they are counterfeit, and so requires all products to contain the code, not just those sold through Amazon.
edit: spelling
Many brands will just print the transparency codes for units destined for Amazon through proper channels...which will be designated by having their own SKU, like brands already do for Costco and Walmart sales.
Product sold through other channels will not have the transparency codes and will be presumed counterfeit.
Nike would have to use a separate SKU for Amazon.
Manufacturers don't need to tag all units unless they sell the same SKU across multiple channels. If they create Amazon-specific SKUs then any non-Amazon SKU would be presumed counterfeit under the new system.